Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

UnifiedGenotyper / Strand Bias (SB)

nguyenqxxnguyenqxx Posts: 3Member
edited January 2013 in Ask the GATK team

Hi,

How to get all SNPs variants with Strand Bias (high SB value) ?

GenomeAnalysisTK.jar -T UnifiedGenotyper  \
-R ucsc.hg19.fasta -D dbsnp_135.hg19.vcf \
-stand_emit_conf 1.5 -stand_call_conf 1.5 \
-o Sample_2.snv.vcf -I Sample_2.recal.bam -nt 10

Thanks,
Q

Post edited by Geraldine_VdAuwera on

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